Ya tomaste en consideración lo siguiente;
Cita: flock() will not work on NFS and many other networked file systems. Check your operating system documentation for more details.
On some operating systems flock() is implemented at the process level. When using a multithreaded server API like ISAPI you may not be able to rely on flock() to protect files against other PHP scripts running in parallel threads of the same server instance!
flock() is not supported on antiquated filesystems like FAT and its derivates and will therefore always return FALSE under this environments (this is especially true for Windows 98 users).
Además ¿Estas seguro de la ruta de tu archivo?
Saludillos.